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GWASStudio: Installation Guide

This guide will walk you through the installation process.

Installation from source

You can install GWASStudio using either the make command (recommended for simplicity) or manually. Choose the method that best fits your workflow.

The make method automates most of the installation steps, making it easier and less error-prone.

Prerequisites

  • Ensure you have make installed on your system.
  • Ensure you have conda or miniconda installed for environment management.

Steps

1. Clone the Repository

Clone the repository to your local machine:

git clone https://github.com/ht-diva/gwasstudio.git
cd gwasstudio

2. Create the Conda Environment

Run the following command to create a dedicated conda environment for GWASStudio:

make create-env

This command reads the environment configuration from base_environment.yml and sets up a clean, isolated environment.

3. Install Dependencies

Install all required dependencies using:

make dependencies

This step ensures that all necessary Python packages and system libraries are installed.

4. Install the Program

Finally, install the program in your conda environment:

make install

This installs the program globally within your conda environment, making it available from the command line.

2. Manual Installation (Without make)

If you prefer not to use make, you can install GWASStudio manually. This method gives you more control over each step.

Prerequisites

Steps

1. Clone the Repository

Clone the repository to your local machine:

git clone https://github.com/ht-diva/gwasstudio.git
cd gwasstudio

1. Create the Conda Environment

Create a new conda environment using the provided configuration file:

conda env create --file base_environment.yml

This command sets up a conda environment with all the base dependencies specified in base_environment.yml.

2. Activate the Conda Environment

Activate the environment with the following commands:

  conda activate gwasstudio

4. Install the program

Use poetry to install the project dependencies (excluding development dependencies) and the program:

  poetry install --without dev

This installs gwasstudio in your active conda environment.